Correct. The MPPS SCP (ppsscpfs) always stores MPPS datasets in Explicit VR Little Endian transfer syntax, independent from the transfer syntax that was used during the network connection. Please also note that each file created by the MPPS SCP represents one MPPS SOP instance, not one message. If you send an N-SET to update an MPPS object, the file will be re-written to reflect the updated status of the MPPS object. Since different N-CREATE and N-SET message could, at least in theory, be sent using different network connections with different transfer syntaxes, there is no real point in keeping the transfer syntax in the file.

Note that there is another MPPS related tool (also not part of the public toolkit) named "PPS manager", which implements the IHE Scheduled Workflow actor of the same name. That tool stores and forwards individual N-CREATE and N-SET messages and also keeps the transfer syntax in the file consistent with the transfer syntax used in the incoming network association. But I guess that won't help you much.